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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | data processing software, data management software, software application, collaboration tool, software resource | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-02-13 10:55:44 | 14 | |||||
|
PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | software resource, source code, data processing software, software application | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip https://sources.debian.org/src/phylip/ |
SCR_006244 | PHYLogeny Inference Package | 2026-02-13 10:55:48 | 3519 | |||||
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Guppy Project Resource Report Resource Website 1+ mentions |
Guppy Project (RRID:SCR_006255) | Guppy Project | organism-related portal, portal, data or information resource, video resource, topical portal | A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record. | adaption, evolution, adaptive evolution, environment, trinidadian guppy, poecilia reticulata, image, natural selection | has parent organization: University of California at Riverside; California; USA | NSF | nlx_151840 | SCR_006255 | 2026-02-13 10:55:47 | 6 | ||||||||
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crowdLabs Resource Report Resource Website 1+ mentions |
crowdLabs (RRID:SCR_006294) | crowdLabs | storage service resource, community building portal, data analysis service, portal, analysis service resource, data or information resource, production service resource, service resource | A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly. | platform, computation, data sharing |
is listed by: FORCE11 is related to: VisTrails |
NSF | nif-0000-06716 | http://www.force11.org/node/4666 | SCR_006294 | crowd Labs | 2026-02-13 10:55:48 | 1 | ||||||
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Plant Ontology Resource Report Resource Website 10+ mentions |
Plant Ontology (RRID:SCR_006494) | PO | data or information resource, ontology, controlled vocabulary, database | Ontology and database that links plant anatomy, morphology and growth and development to plant genomics data.Plant Ontology Consortium develops, curates and shares controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing semantic framework for meaningful cross species queries across databases. PO is under active development to expand to encompass terms and annotations from all plants. | obo, gene, development, anatomy, morphology, growth, genomics, database |
has parent organization: Oregon State University; Oregon; USA has parent organization: Cornell University; New York; USA |
NSF 0822201; NSF 0321685 |
PMID:18628842 PMID:18194960 |
SCR_006844, nlx_55564 | SCR_006494 | Plant Ontology Browser, PO Browser, Plant Ontology Consortium Database, PO Database, Plant Ontology Database, POC Database | 2026-02-13 10:55:51 | 31 | ||||||
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Integrated Earth Data Applications Resource Report Resource Website 1+ mentions |
Integrated Earth Data Applications (RRID:SCR_006739) | IEDA | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR. | map, ocean, earth, polar, sciences, ocean sciences, earth sciences, polar sciences, doi, global geochemistry, marine geoscience |
has parent organization: Columbia University; New York; USA is parent organization of: Marine Geoscience Data System is parent organization of: Global-Multi Resolution Topography Image Service is parent organization of: Global-Multi Resolution Topography Grid Service |
NSF | The community can contribute to this resource, Free, Open unspecified license | nlx_156096 | SCR_006739 | 2026-02-13 10:55:53 | 1 | |||||||
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Rice Genome Annotation Resource Report Resource Website 1000+ mentions |
Rice Genome Annotation (RRID:SCR_006663) | Osa1 | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes | rice, oryza sativa, maize, corn, zea mays, wheat, triticum aestivum, gene, genome, annotation, FASEB list |
is listed by: OMICtools has parent organization: Michigan State University; Michigan; USA |
NSF DBI-0321538; NSF DBI-0834043 |
PMID:17145706 | Acknowledgement requested | OMICS_01563, nif-0000-31459 | http://rice.tigr.org | http://rice.plantbiology.msu.edu/pseudomolecules/info.shtml | SCR_006663 | Rice Genome Annotation Project, MSU Rice Genome Annotation Project Database and Resource | 2026-02-13 10:55:52 | 1423 | |||
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data repository, storage service resource, data or information resource, service resource, database | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NSF EF0843229; NIGMS U24 GM144232 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-02-13 10:55:56 | 14 | ||||
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iDEP: Integrated Differential Expression and Pathway analysis Resource Report Resource Website 1+ mentions |
iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) | iDEP | software resource, web application | Integrated web application for differential expression and pathway analysis of RNA-Seq data. | differential expression, pathway analysis, RNA-Seq data, | NIGMS GM083226; NSF ; State of South Dakota |
PMID:30567491 | Free, Freely available | SCR_027373 | 2026-02-12 09:49:12 | 8 | ||||||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, software resource, data processing software, software application | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/ https://bio.tools/gasv |
SCR_000061 | Geometric Analysis of Structural Variants | 2026-02-13 10:54:36 | 4 | ||||
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forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software resource, simulation software, software application | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-02-13 10:54:43 | 0 | |||||
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Human Brain Atlas Resource Report Resource Website 1+ mentions |
Human Brain Atlas (RRID:SCR_006131) | Human Brain Atlas | data or information resource, atlas, video resource | A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp | human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus |
is used by: NIF Data Federation has parent organization: Michigan State University; Michigan; USA |
NSF IBN 0131267; NSF 0131826; NSF 0131028 |
Copyrighted, Public, Request that you secure their permission, Acknowledgement required | nif-0000-00088 | SCR_006131 | MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas | 2026-02-12 09:44:10 | 3 | ||||||
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XSEDE - Extreme Science and Engineering Discovery Environment Resource Report Resource Website 10+ mentions |
XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) | XSEDE | data or information resource, portal | XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools. | data sharing, computing, supercomputer, data, tool, visualization, data analysis, cyberinfrastructure, digital service, high performance computing, high throughput computing, visualization, storage, data service |
is related to: Neuroscience Gateway has parent organization: San Diego Supercomputer Center |
NSF OCI-1053575 | nlx_151554, grid.501421.3 | https://ror.org/05524hb64 | SCR_006091 | XSEDE - Extreme Science Engineering Discovery Environment, Extreme Science and Engineering Discovery Environment | 2026-02-12 09:44:24 | 27 | ||||||
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Hymenoptera Anatomy Ontology Resource Report Resource Website 1+ mentions |
Hymenoptera Anatomy Ontology (RRID:SCR_003340) | HAO | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants) | owl, anatomy, organismal |
is listed by: BioPortal is listed by: OBO |
NSF DBI 0850223 | Free, Freely available | nlx_157435 | http://purl.bioontology.org/ontology/HAO http://purl.obolibrary.org/obo/hao.owl |
SCR_003340 | 2026-02-12 09:43:34 | 2 | ||||||
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Planet Microbe Resource Report Resource Website 1+ mentions |
Planet Microbe (RRID:SCR_024478) | software resource, web application | Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data. | data discovery, curated oceanographic sequencing, biological and physiochemical measurements, water samples, marine microbiology, discover and analyze interconnected 'omics and environmental data, | has parent organization: University of Arizona; Arizona; USA | NSF | PMID:32735679 | Free, Freely available | https://github.com/hurwitzlab/planet-microbe-app | SCR_024478 | 2026-02-12 09:48:42 | 2 | |||||||
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iSamples Resource Report Resource Website 1+ mentions |
iSamples (RRID:SCR_021750) | data or information resource, portal, project portal | Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications. | Align physical sample identifiers, physical sample identifiers, align identifiers | NSF 2004839; NSF 2004562; NSF 2004642; NSF 2004815 |
DOI:10.1093/gigascience/giab028 | Free, Freely available | https://zenodo.org/communities/isamples?page=1&size=20 | SCR_021750 | internet of Samples | 2026-02-12 09:47:16 | 1 | |||||||
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runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | software resource, web application | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NSF ; NIH |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | 2026-02-12 09:47:39 | 3 | |||||||
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BioSimulations Resource Report Resource Website |
BioSimulations (RRID:SCR_018733) | software resource, web application | Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. | Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA has parent organization: University of Connecticut; Connecticut; USA |
NIBIB P41 EB023912; NSF ; NIGMS |
Restricted | biotools:biosimulations | https://bio.tools/biosimulations | SCR_018733 | 2026-02-12 09:47:05 | 0 | |||||||
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Rcorrector Resource Report Resource Website 10+ mentions |
Rcorrector (RRID:SCR_022011) | data analysis software, software resource, data processing software, software application | Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads. | RNA-seq, k-mer, random sequencing errors correction, kmer based error correction, RNA-seq data, sequencing data, nonuniform read coverage, Illumina RNAseq reads error correction | NSF ABI1159078; NSF ABI1356078 |
DOI:10.1186/s13742-015-0089-y | Free, Available for download, Freely available | SCR_022011 | RNA-seq error CORRECTOR | 2026-02-13 10:58:37 | 32 | ||||||||
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Tandem Repeats Finder Resource Report Resource Website 100+ mentions |
Tandem Repeats Finder (RRID:SCR_022193) | TRF | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences. | nucleotides pattern, pattern copies, DNA tandem repeat, DNA sequences, locate tandem repeats | NSF CCR9623532 | PMID:9862982 | Free, Available for download, Freely available | https://tandem.bu.edu/trf/trf.html | SCR_022193 | 2026-02-13 10:58:39 | 421 |
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